Draft Genome Sequences of Two Campylobacter jejuni Clinical Isolates,NW and D2600

The Campylobacter jejuni human clinical isolates NW and D2600 colonized C57BL/6 interleukin-10-deficient (IL-10^−/−) mice without inducing a robust inflammatory response (J. A. Bell et al., BMC Microbiol. 9:57, 2009). We announce draft genome sequences of NW and D2600 to facilitate comparisons with strains that induce gastrointestinal inflammation in this mouse model.     

Evolution of the Mitochondrial Genome in Cephalochordata as Inferred from Complete Nucleotide Sequences from Two Epigonichthys Species

Complete mitochondrial (mt) DNA sequences of two lancelets, Epigonichthys maldivensis and E. lucayanus, were compared with those of two Branchiostoma lancelets and several deuterostomes previously surveyed. The mt-gene order of E. lucayanus was quite different from that of E. maldivensis, the latter being identical to the two Branchiostoma species. A remarkable genomic change in E. lucayanus mtDNA was an inversion, indicating the possibility of recombination of the mt-genome. Gene rearrangements, probably attributable to tandem genome duplications and subsequent random deletions, were observed in two parts. Short major unassignable sequences of the examined lancelets were regarded as a part of putative regulative elements, judging from some sequence similarity to the conserved sequence block (CSB) in mammalian mtDNA. The considerable mt-genome reorganization in E. lucayanus seemed to have affected the nucleotide substitution pattern, suggested by base composition analyses. The present analysis also suggested that AGR codons in lancelet mtDNA were likely to correspond to serine residue, rather than glycine. Furthermore, the AGG codon, so far reputed to be unassignable in lancelet mtDNA, was found twice in E. maldivensis, indicating the availability of all four AGN codons in some lancelets. This finding lends support to an alternative hypothesis regarding the evolutionary history of AGR-codon assignment in extant chordates, rather than that previously proposed. A molecular phylogenetic tree of the Epigonichthys and Branchiostoma species based on DNA sequences of the 13 mt-protein genes doubted the monophyly of the former genus, unlike the prevailing classification based on their different gonadal arrangements.Reviewing Editor: Dr. Axel Meyer     

Genome Sequences of Pseudomonas luteola XLDN4-9 and Pseudomonas stutzeri XLDN-R,Two Efficient Carbazole-Degrading Strains

Pseudomonas luteola XLDN4-9 and Pseudomonas stutzeri XLDN-R are two efficient carbazole-degrading pseudomonad strains. Here we present 4.63- and 4.70-Mb assemblies of their genomes. Their annotated key genes for carbazole catabolism are similar, which may provide further insights into the molecular mechanism of carbazole degradation in Pseudomonas.     

Genome Sequences of Three Live Attenuated Vaccine Strains of Brucella Species and Implications for Pathogenesis and Differential Diagnosis

Live attenuated vaccines play essential roles in the prevention of brucellosis. Here, we report the draft genome sequences of three vaccine strains, Brucella melitensis M5-10, B. suis S2-30, and B. abortus 104M. Primary genome sequence analysis identified mutations, deletions, and insertions which have implications for attenuation and signatures for differential diagnosis.     

Draft Genome Sequences of Two Streptococcus pyogenes Strains Involved in Abnormal Sharp Raised Scarlet Fever in China, 2011

A scarlet fever outbreak caused by Streptococcus pyogenes occurred in China in 2011. To determine the genomic features of the outbreak strains, we deciphered genomes of two strains isolated from the regions with the highest incidence rates. The sequences will provide valuable information for comprehensive study of mechanisms related to this outbreak.     

烟草花叶病毒（普通株中国分离物）及其弱毒苗—N14（番茄株）组织 …

用双脱氧未端经终止法对侵染性烟草共现毒普通株中国分离物（ＴＭＶ－ｖｉｒｌｇａｒ,Ｃｈｉｎｅｓｅ ｌｓｏｂｌａｔｅ,ＴＭＶ－Ｃｖ）和番茄株弱毒轩ＴＭＶ－Ｎ１４（Ａｔｔｅｎｕａｔｅｄ ＴＭＶ ｖａｃｃｉｎｅ ｓｔｒａｉｎ）基因组ｃＤＮＡｓ的核苷酸全序列进行了测定,并分析和比较了其基因组的结构和特征。结果表明：普通株基因组（Ｇｅｎｂａｎｋ接收号：ＡＦ１６５１９０）为６３９５个核苷酸：４个功能性开放阅读框     

烟草花叶病毒(普通株中国分离物)及其弱毒疫苗N14(番茄株)基因组侵染性cDNA核苷酸全序列测定与分析

用双脱氧末端终止法对侵染性烟草花叶病毒普通株中国分离物(TMV-vulgar,Chinese Isolate,TMVCv)和番茄株弱毒疫苗TM-N14(Attenuated TMV vaccine strain)基因组cDNAs的核苷酸全序列进行了测定,并分析和比较了其基因组的结构和特征。结果表明：普通株基因组(Genbank接收号：AF165190)为6395个核苷酸;4个功能性开放阅读框架(ORF),分别编码126kD/183kD的复制酶、30kD运动蛋白和17.6kD外壳蛋白。弱毒疫苗TMV-N14基因组(Genbank接收号：AF155507)为6384个核苷酸;5个功能性ORF分别编码985kD/126kD/183kD的复制酶、27kD运动蛋白和17.6kD外壳蛋白。与参比序列核苷酸和氨基酸序列比较：普通株核苷酸序列同源率为99.4%;推断的复制酶与运动蛋白分别有5个和2个氨基酸残基不同。TMV-N14核苷酸序列同源率为99.7%;核苷酸位置2670～2672和5632～5634分别发生乳石(Opal)突变(UGA)和赭石(Ochre)突变(UAA);推断复制酶有13个氨基酸残基发生了变异。     

Genome Sequences of Two Multidrug-Resistant Acinetobacter baumannii Strains Isolated from a Patient before and after Treatment with Tigecycline

Acinetobacter baumannii is a Gram-negative bacterium which emerged as a significant nosocomial pathogen worldwide. To investigate the molecular basis of the tigecycline-resistant mechanism, we determined the genome sequences of two multidrug-resistant A. baumannii strains isolated from a patient before and after treatment with tigecycline.     

Draft Genome Sequences of Four Axenic Mycoplasma genitalium Strains Isolated from Denmark,Japan, and Australia

The DNA genome of Mycoplasma genitalium currently represents the smallest of all known human bacterial pathogens. Despite their clinical importance in sexually transmitted infection and relevance as model bacterial pathogens, genomic diversity among M. genitalium strains worldwide is unknown. Herein we present the complete draft genome sequences of four geographically diverse strains of M. genitalium.     

Genome Sequences of Pelagibaca bermudensis HTCC2601T and Maritimibacter alkaliphilus HTCC2654T,the Type Strains of Two Marine Roseobacter Genera

Pelagibaca bermudensis HTCC2601^T and Maritimibacter alkaliphilus HTCC2654^T represent two marine genera in the globally significant Roseobacter clade of the Alphaproteobacteria. Here, we present the genome sequences of these organisms, isolated from the Sargasso Sea using dilution-to-extinction culturing, which offer insight into the genetic basis for the metabolic and ecological diversity of this important group.Organisms from the Roseobacter clade of the Alphaproteobacteria are numerically significant in the world''s oceans and have been found in a wide range of habitats (1, 3). Using previously described high-throughput dilution-to-extinction culturing (6, 13), the marine Roseobacter strains Pelagibaca bermudensis HTCC2601^T and Maritimibacter alkaliphilus HTCC2654^T were isolated in low-nutrient heterotrophic medium (LNHM) (4) from surface water collected at the Bermuda Atlantic Time-Series Study (BATS) site in the western Sargasso Sea (5, 9). As the type strains for two genera of this globally prolific Roseobacter group, P. bermudensis and M. alkaliphilus were selected for shotgun genome sequencing at the J. Craig Venter Institute through the Moore Foundation Microbial Genome Sequencing Project (http://www.moore.org/microgenome). Draft genomes of P. bermudensis and M. alkaliphilus, with 103 and 46 contigs, respectively, were annotated and analyzed through the Joint Genome Institute IMG/M website (http://img.jgi.doe.gov/cgi-bin/pub/main.cgi) (10).The draft genomes of P. bermudensis and M. alkaliphilus comprise 5,425,920 and 4,529,231 bases, 5,522 and 4,764 predicted open reading frames (ORFs), and 66.44% and 64.13% G+C content, respectively. The P. bermudensis genome is predicted to contain 56 tRNA genes, five 5S rRNA genes, four 16S rRNA genes, and five 23S rRNA genes, and that of M. alkaliphilus 49 tRNA genes and one each of the 5S, 16S, and 23S rRNA genes. Both genomes have putative genes for complete glycolysis and Entner-Doudoroff pathways, a complete tricarboxylic acid cycle, and predicted metabolic pathways for the oxidation of C₁ compounds. Both have predicted genes for the synthesis of most essential amino acids and some vitamins and cofactors. Each has putative genes for the utilization of fructose, sucrose, and mannose, confirmed in physiological testing of P. bermudensis (5) but not for M. alkaliphilus (9). P. bermudensis contains a predicted complete RuBisCO complex, unique to the sequenced Roseobacter species (12, 15), a complete assimilatory nitrate reduction pathway, and several type VI secretion genes. M. alkaliphilus is predicted to have complete nitrate reduction pathways to both N₂ and ammonia and most type IV secretion genes. Both are predicted to have complete sec pathways and large numbers of ABC transporters (362 in P. bermudensis and 224 in M. alkaliphilus), similar to other Roseobacter strains (15).M. alkaliphilus was named because of its alkaline growth optimum at pH 10. Na⁺/H⁺ antiporters have been shown to be involved in conferring alkaliphilic phenotypes for a variety of organisms by increasing internal cellular H⁺ concentrations in alkaline conditions where Na⁺ is present (2, 7, 8, 14, 16, 17). As expected, the genome of M. alkaliphilus contains two putative Na⁺/H⁺ antiporters, one homologous to nhaP, important for alkaliphily in several strains (2, 16, 17), and another located adjacent to predicted ABC transporter genes for capsular polysaccharide export.     

Ecological Assessment of Two Species of Potamonautid Freshwater Crabs from the Eastern Highlands of Zimbabwe,with Implications for Their Conservation

The spatial ecology of freshwater crabs and their conservation status is largely understudied in Africa. An ecological assessment was conducted at 104 localities in 51 rivers and/or streams in the Eastern Highlands of Zimbabwe whereby the distribution and abundances of freshwater crab species were mapped and the possible drivers of the observed trends in population structure explored. In addition, information on crab utilisation as a food resource by local communities was assessed via face to face interviews across the region. Finally, the conservation status of each species was assessed using the IUCN Red List criteria. Only two crab species Potamonautes mutareensis and Potamonautes unispinus were recorded within the region of study. Potamonautes mutareensis was largely restricted to less impacted environments in the high mountainous river system, whereas P. unispinus was found in low laying areas. In stretches of river where both species were found to co-occur, the species were never sampled from the same site, with P. mutareensis occurring in shallower, faster flowing environments and P. unispinus in deeper, slow flowing sites. Interview results revealed that the local communities, particularly in the southern part of the Eastern Highlands around the Chipinge area, had a considerable level of utilisation (55% of households) on the harvesting of crabs for household consumption during the non-agricultural season (May to September). Results from the IUCN Red List assessment indicate that both species should be considered as “Least Concern”. Threats to freshwater crabs in the Eastern Highlands, however, include widespread anthropogenic impacts such as habitat destruction associated with gold and diamond mining, inorganic and organic pollution and possibly exploitation for human consumption. The current study provides important information and insight towards the possible development of a freshwater crab conservation action plan within the region.     

Complete Genome Sequences of Two Persicivirga Bacteriophages, P12024S and P12024L

The phylum Bacteroidetes is one of the major bacterial phyla in marine environments, where bacteriophages are highly abundant. Bacteriophages infecting members of the phylum Bacteroidetes, however, have not been well represented in public genome databases. Here we announce the genome sequences of two bacteriophages, P12024S and P12024L, that were isolated from coastal seawater and lytically infect Persicivirga sp. IMCC12024, a marine Bacteroidetes bacterium.     

Draft Genome Sequences of Helicobacter pylori Isolates from Malaysia,Cultured from Patients with Functional Dyspepsia and Gastric Cancer

Helicobacter pylori is the main bacterial causative agent of gastroduodenal disorders and a risk factor for gastric adenocarcinoma and mucosa-associated lymphoid tissue (MALT) lymphoma. The draft genomes of 10 closely related H. pylori isolates from the multiracial Malaysian population will provide an insight into the genetic diversity of isolates in Southeast Asia. These isolates were cultured from gastric biopsy samples from patients with functional dyspepsia and gastric cancer. The availability of this genomic information will provide an opportunity for examining the evolution and population structure of H. pylori isolates from Southeast Asia, where the East meets the West.     

Whole Genome Sequences of Two Xylella fastidiosa Strains (M12 and M23) Causing Almond Leaf Scorch Disease in California

Xylella fastidiosa is a Gram-negative plant-pathogenic bacterium causing many economically important diseases, including almond leaf scorch disease (ALSD) in California. Genome information greatly facilitates research on this nutritionally fastidious organism. Here we report the complete genome sequences of two ALSD strains of this bacterium, M12 and M23.Xylella fastidiosa is a Gram-negative and nutritionally fastidious plant-pathogenic bacterium that causes almond leaf scorch disease (ALSD) and Pierce''s disease (PD) of grapevine. In 2003, we isolated two ALSD strains of X. fastidiosa from almond trees in Kern County in the San Joaquin Valley of California. Strain M12 caused only ALSD, and strain M23 caused both ALSD and PD. 16S rRNA gene sequences were analyzed; strain M12 was regarded as A genotype and strain M23 as G genotype (1), corresponding to X. fastidiosa subsp. multiplex and X. fastidiosa subsp. fastidiosa (4), respectively.Genomic DNAs of X. fastidiosa strains M12 and M23 were extracted from pure culture in PW medium (1). The random shotgun method was used for genome sequencing. Large-insert (40-kb), medium-insert (8-kb), and small-insert (3-kb) random libraries were partially sequenced, and sequences were assembled with parallel Phrap (High Performance Software, LLC). Possible misassemblies were corrected with the Dupfinisher software program (2). Gaps between contigs were closed by custom primer walking through PCR amplification. Annotation of the assembled genome sequence was carried out with the genome annotation system Oak Ridge Genome Annotation and Analysis (ORGAA) Pipelines and JGI Integrated Microbial Genomes (IMG) server (3). A combined gene prediction strategy was applied by means of the GLIMMER 2.0 system and the CRITICA program suite, along with postprocessing by the RBSfinder tool. tRNA genes were identified using the tRNAscan-SE server. The deduced proteins were functionally characterized by automated searches in public databases, including SWISS-PROT and TrEMBL, Pfam, TIGRFAM, InterPro, and KEGG. Additionally, the SignalP, helix-turn-helix, and TMHMM software programs were applied. Finally, each gene was functionally classified by assigning a clusters of orthologous groups (COG) number and corresponding COG category and gene ontology numbers. Detailed information about the genome properties, genome annotation, and its related references can be obtained from the JGI Integrated Microbial Genomes website at http://img.jgi.doe.gov/pub/.The genome of X. fastidiosa M12 consists of a single, circular, 2,475,130-nucleotide (nt) chromosome that has a GC content of 51.9%. A total of 2,368 protein-encoding genes are predicted, 2,104 of which have been assigned a tentative function. The genome of X. fastidiosa M23 consists of a single, circular, 2,535,690-nt chromosome that has a GC content of 51.7%. A total of 2,280 protein-encoding genes are predicted, 2,161 of which have been assigned a tentative function. In addition, a circular plasmid of 38,297 nt, pXFAS01, with a GC content of 49%, was also identified in strain M23 but was absent in strain M12. Both strains had two identical rRNA operons in their chromosomes.     

Kinetics of Transmission, Infectivity, and Genome Stability of Two Novel Mouse Norovirus Isolates in Breeding Mice

Murine noroviruses are a recently discovered group of viruses found within mouse research colonies in many animal facilities worldwide. In this study, we used 2 novel mouse norovirus (MNV) wildtype isolates to examine the kinetics of transmission and tissue distribution in breeding units of NOD.CB17-Prkdc^scid/J and backcrossed NOD.CB17-Prkdc^scid/J × NOD/ShiLtJ (N1) mice. Viral shedding in feces and dissemination to tissues of infected offspring mice were monitored by RT-PCR over a 6-wk period postpartum. Histologic sections of tissues from mice exposed to MNV were examined for lesions and their sera monitored for the presence of antibodies to MNV. Viruses shed in feces of parental and offspring mice were compared for sequence homology of the Orf2 gene. Studies showed that the wildtype viruses MNV5 and MNV6 behaved differently in terms of the kinetics of transmission and distribution to tissues of offspring mice. For MNV5, virus transmission from parents to offspring was not seen before 3 wk after birth, and neither isolate was transmitted between cages of infected and control mice. Susceptibility to infection was statistically different between the 2 mouse strains used in the study. Both immunodeficient NOD.CB17-Prkdc^scid/J mice and NOD.CB17-Prkdc^scid/J × NOD/ShiLtJ offspring capable of mounting an immune response shed virus in their feces throughout the 6-wk study period, but no gross or histologic lesions were present in infected tissues. Progeny viruses isolated from the feces of infected offspring showed numerous mutations in the Orf2 gene for MNV5 but not MNV6. These results confirm previous studies demonstrating that the biology of MNV in mice varies substantially with each virus isolate and mouse strain infected.Abbreviations: MNV, murine norovirus; MLN, mesenteric lymph nodes; NOD-scid, NOD.CB17-Prkdc^scid/J; VP1, viral protein 1The recent discovery of murine-specific noroviruses¹⁵ has stimulated concern in the laboratory animal health community regarding the potential for this group of viruses to cause disease in breeding colonies of mice or to negatively impact research with mice from norovirus infected colonies. Current knowledge of the biology of noroviruses in mice (MNV) is constrained by the limited number of virus isolates and mouse strains studied. One study¹⁵described the biologic and physicochemical properties of the original MNV1 isolated from mice deficient in a specific innate immune function. More recently, this innate immune deficiency has been mapped to STAT1 regulation of IFNαβ secretion.²¹Previous work¹⁵ demonstrated that inoculation of MNV1 into mouse strains deficient in the acquired immune response (129 RAG 2^−/−, B6 RAG1^−/−) resulted in the development of persistent infections with no evidence of disease, whereas inoculation of fully immunocompetent mice (129S6/SvEvTac) resulted in rapid elimination of MNV1, with viral RNA undetectable in the viscera by 3 d after inoculation. More recently, infections of outbred immunocompetent mouse strains with 3 wildtype isolates of MNV obtained from different geographic areas of the United States have been described.¹¹ Virus was detected in the feces and tissue of infected mice throughout the 8-wk study, suggesting that some isolates of MNV may persistently infect immunocompetent mice.The purpose of the present investigation was to extend the current knowledge of MNV by using 2 isolates of the virus in mouse strains that have not been previously used as infection models for MNV. We examined natural virus transmission from infected breeders to offspring, kinetics of infection within litters of infected breeding mice, and the pathogenesis of infection in breeding colonies of mice. In addition, we examined the effect of virus passage from parents to offspring on genomic stability of these 2 viral isolates. Exposure of offspring of immunodeficient mice and immunocompetent mice to the 2 different isolates of MNV resulted in different patterns of virus transmission, susceptibility to infection and kinetics of infection as shown by the progressive spread of virus within litters and in intestinal and extraintestinal tissues. MNV was shed persistently in the feces of all mice tested regardless of immune status, and viral progeny isolated from offspring mice contained genome sequence differences from the parent virus in the Orf2 gene, an area of the MNV genome known to be susceptible to mutations.     

Host Selectivity and Genetic Variation of Discula umbrinella Isolates from Two Oak Species: Analyses of Intergenic Spacer Region Sequences of Ribosomal DNA

Discula umbrinella, a fungal endophyte of oak species, colonizes and reproduces on leaves of Quercus alba and Q. rubra in forest ecosystems. Twenty-nine isolates collected from leaves of both oak species (16 from Q. alba and 13 from Q. rubra) were assayed for oak species preference and genetic variation based on primer-specific polymerase chain reactions for the intergenic spacer region (IGS) of ribosomal DNA. DNA sequencing of the polymerase chain reaction products revealed a 10-bp insertion (237–247 bp) at the 3′ end of the IGS region present in nine isolates and absent in 20 of the isolates. Phylogenetic analysis of the IGS region using the neighbor-joining method identified IGS groups (groups I–V) based on single nucleotide sequence differences. Host selectivity and geographic origin of isolates were correlated in some instances with the IGS groups. Isolates within each IGS group were further analyzed for nucleotide polymorphisms to confirm genotype identity and genotype diversity. Ten different genotypes (V_a–V_j) were identified among the isolates analyzed. Genotype diversity was greatest in IGS groups I, IV, and V. Seventy percent of the genotypes (V_c, V_d, V_e, V_f, V_g,V_i, and V_j) contained isolates with single tree species preferences.     

Genome Sequences of Burkholderia sp. Strains CCGE1002 and H160, Isolated from Legume Nodules in Mexico and Brazil

The genome sequences of Burkholderia sp. strains CCGE1002 from Mexico and H160 from Brazil, isolated from legume nodules, are reported. Their gene contents in relation to plant-microbe interactions and xenobiotic degradation are discussed.     

Morphology,Ontogeny, and Molecular Phylogeny of Two Freshwater Species of Deviata (Ciliophora,Hypotrichia) from Southern China

The morphology and partial morphogenesis of two freshwater hypotrichous ciliates, Deviata brasiliensis Siqueira‐Castro et al., 2009 and Deviata rositae Küppers et al., 2007, isolated from southern China, were investigated using live observation and protargol staining. Our populations resemble the original ones in terms of their live characters and ciliary patterns. The main determinable morphogenetic features of D. brasiliensis basically correspond with those of the type population. However, the origin of anlage V for either proter or opisthe is ambiguous: whether anlage V for the proter originates from parental frontoventral row 2 (the same as in the original population) or parental frontoventral row 3 (the same as in Deviata abbrevescens) or even de novo is not clear; the anlage V for the opisthe is possibly derived from frontoventral row 3 and further migrates to frontoventral row 2, like that in D. abbrevescens. In addition, the SSU rRNA gene was first sequenced for both species. Molecular phylogenetic analyses suggest that the genus Deviata is non‐monophyletic and has a close relationship with Perisincirra paucicirrata.